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Series GSE102237 Query DataSets for GSE102237
Status Public on Aug 11, 2017
Title Poly(ADP-ribosyl)ation dependent changes in CTCF-chromatin binding and gene expression in breast cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary CTCF is an evolutionary conserved and ubiquitously expressed architectural protein, which regulates a plethora of cellular functions using different molecular mechanisms. The main form of CTCF with an apparent molecular mass of 130 kDa (CTCF130) has been extensively studied, however the properties of CTCF180, highly modified by poly(ADP-ribosyl)ation (PARylation) are not well understood. In this study we performed ChIP-seq and RNA-seq analyses in breast cells 226LDM, proliferating (with CTCF130 as the most abundant CTCF form) and arrested in the cell cycle (with only CTCF180). A dramatic reorganization of CTCF binding was observed during this transition, whereby CTCF was evacuated from many sites ("lost" group), although some sites retained modified CTCF ("common") and others acquired CTCF180 ("gained"). The classic CTCF binding motifs were identified for the former two groups, whereas the latter had no CTCF binding motif. Changes in CTCF occupancies in lost/common (but not gained) sites were associated with increased chromatin densities and altered expression from the neighboring genes. We propose a model integrating CTCF130/180 transition with CTCF-DNA binding and gene expression patterns, and functional outcomes. This study issues an important cautionary note concerning design and interpretation of any experiments using cells and tissues where CTCF180 may be present.
 
Overall design ChIP-Seq and RNA-Seq analyses to investigate CTCF binding, histone patterns and gene expression profiles in breast cells, 226LDM, proliferating (with CTCF130 as the most abundant CTCF form) and chemically arrested in the cell cycle (with only CTCF180)
 
Contributor(s) Pavlaki I, Docquier F, Chernukhin I, Teif VB, Klenova E
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Submission date Aug 03, 2017
Last update date May 15, 2019
Contact name Vladimir B Teif
E-mail(s) vteif@essex.ac.uk
Organization name University of Essex
Street address Wivenhoe Park
City Colchester
ZIP/Postal code CO4 3SQ
Country United Kingdom
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (18)
GSM2731525 CTCF control replicate 1
GSM2731526 CTCF control replicate 2
GSM2731527 H3K9me3 control replicate 1
Relations
BioProject PRJNA397068
SRA SRP114785

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE102237_IP01andIP02_control_IP07andIP08_MACS_peaks.bed.gz 142.6 Kb (ftp)(http) BED
GSE102237_IP05andIP06_control_IP07andIP08_MACS_peaks.bed.gz 67.7 Kb (ftp)(http) BED
GSE102237_IP09andIP10_control_IP15andIP16_MACS_peaks.bed.gz 33.1 Kb (ftp)(http) BED
GSE102237_IP13andIP14_control_IP15andIP16_MACS_peaks.bed.gz 21.0 Kb (ftp)(http) BED
GSE102237_deseq_Pavlaki_differential_expression.tab.gz 764.8 Kb (ftp)(http) TAB
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